UniProt Knowledgebase: a Hub of Integrated Protein Data

Overview

Journal Database (Oxford)

Specialty Biology

Date 2011 Mar 31

PMID 21447597

Citations 791

Authors

Michele Magrane

Affiliations

Soon will be listed here.

Abstract

The UniProt Knowledgebase (UniProtKB) acts as a central hub of protein knowledge by providing a unified view of protein sequence and functional information. Manual and automatic annotation procedures are used to add data directly to the database while extensive cross-referencing to more than 120 external databases provides access to additional relevant information in more specialized data collections. UniProtKB also integrates a range of data from other resources. All information is attributed to its original source, allowing users to trace the provenance of all data. The UniProt Consortium is committed to using and promoting common data exchange formats and technologies, and UniProtKB data is made freely available in a range of formats to facilitate integration with other databases. Database URL: http://www.uniprot.org/

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References

Leinonen R, Diez F, Binns D, Fleischmann W, Lopez R, Apweiler R . UniProt archive. Bioinformatics. 2004; 20(17):3236-7. DOI: 10.1093/bioinformatics/bth191. View

Dowell R, Jokerst R, Day A, Eddy S, Stein L . The distributed annotation system. BMC Bioinformatics. 2001; 2:7. PMC: 58584. DOI: 10.1186/1471-2105-2-7. View

Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry J . Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000; 25(1):25-9. PMC: 3037419. DOI: 10.1038/75556. View

Aranda B, Achuthan P, Alam-Faruque Y, Armean I, Bridge A, Derow C . The IntAct molecular interaction database in 2010. Nucleic Acids Res. 2009; 38(Database issue):D525-31. PMC: 2808934. DOI: 10.1093/nar/gkp878. View

Jimenez R, Quinn A, Garcia A, Labarga A, ONeill K, Martinez F . Dasty2, an Ajax protein DAS client. Bioinformatics. 2008; 24(18):2119-21. DOI: 10.1093/bioinformatics/btn387. View

Notredame C . Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 2002; 3(1):131-44. DOI: 10.1517/14622416.3.1.131. View

Kretschmann E, Fleischmann W, Apweiler R . Automatic rule generation for protein annotation with the C4.5 data mining algorithm applied on SWISS-PROT. Bioinformatics. 2001; 17(10):920-6. DOI: 10.1093/bioinformatics/17.10.920. View

Altschul S, Madden T, Schaffer A, Zhang J, Zhang Z, Miller W . Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25(17):3389-402. PMC: 146917. DOI: 10.1093/nar/25.17.3389. View

Leinonen R, Akhtar R, Birney E, Bonfield J, Bower L, Corbett M . Improvements to services at the European Nucleotide Archive. Nucleic Acids Res. 2009; 38(Database issue):D39-45. PMC: 2808951. DOI: 10.1093/nar/gkp998. View

10.

Benson D, Karsch-Mizrachi I, Lipman D, Ostell J, Sayers E . GenBank. Nucleic Acids Res. 2009; 38(Database issue):D46-51. PMC: 2808980. DOI: 10.1093/nar/gkp1024. View

11.

Velankar S, Best C, Beuth B, Boutselakis C, Cobley N, Sousa Da Silva A . PDBe: Protein Data Bank in Europe. Nucleic Acids Res. 2009; 38(Database issue):D308-17. PMC: 2808887. DOI: 10.1093/nar/gkp916. View

12.

Golovin A, Henrick K . MSDmotif: exploring protein sites and motifs. BMC Bioinformatics. 2008; 9:312. PMC: 2491636. DOI: 10.1186/1471-2105-9-312. View

13.

Notredame C . Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol. 2007; 3(8):e123. PMC: 1963500. DOI: 10.1371/journal.pcbi.0030123. View

14.

Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K . DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Res. 2009; 38(Database issue):D33-8. PMC: 2808917. DOI: 10.1093/nar/gkp847. View

15.

Hunter S, Apweiler R, Attwood T, Bairoch A, Bateman A, Binns D . InterPro: the integrative protein signature database. Nucleic Acids Res. 2008; 37(Database issue):D211-5. PMC: 2686546. DOI: 10.1093/nar/gkn785. View

16.

Pruitt K, Tatusova T, Klimke W, Maglott D . NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 2008; 37(Database issue):D32-6. PMC: 2686572. DOI: 10.1093/nar/gkn721. View

17.

Notredame C, Higgins D, Heringa J . T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000; 302(1):205-17. DOI: 10.1006/jmbi.2000.4042. View

18.

Vilella A, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E . EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res. 2008; 19(2):327-35. PMC: 2652215. DOI: 10.1101/gr.073585.107. View

19.

Gattiker A, Michoud K, Rivoire C, Auchincloss A, Coudert E, Lima T . Automated annotation of microbial proteomes in SWISS-PROT. Comput Biol Chem. 2003; 27(1):49-58. DOI: 10.1016/s1476-9271(02)00094-4. View

20.

Blake J, Bult C, Kadin J, Richardson J, Eppig J . The Mouse Genome Database (MGD): premier model organism resource for mammalian genomics and genetics. Nucleic Acids Res. 2010; 39(Database issue):D842-8. PMC: 3013640. DOI: 10.1093/nar/gkq1008. View